This certainly won't be good press for Citi, which is striving to become the "world's digital bank." The iPad application was also launched just last summer, and problems seemed to have started immediately afterwards.

A Citi spokesman said only 2% of iPad transactions were double charged and that they plan to reimburse all the customers that were affected by the issue. The problem has reportedly been fixed.

The double charges allegedly started in July of last year but Citi wasn't alerted to the issues until December. There is also confusion over the extent of the double charging problem, as some customers said they had been double charged despite not using the iPad app, according to DealBook.